In Indonesia security analysts say there is a growing connection between terrorist groups and Islamic fundamentalist organizations that do not overtly advocate violence. They say this new collaboration has resulted in more attacks against Christians and members of the Ahmadiyah religious sect.

Security analyst Sidney Jones with the International Crisis Group says after Indonesian security forces dismantled a terrorist training camp in Aceh last year, remaining cells reassessed their strategy.

For years they have tried and failed to impose an Islamic state through the violent overthrow of the government. She says they have now begun to look at how effective legal Islamic groups have been in pressuring the government to pass a strong anti-pornography law and banning the Ahmadiyah sect from propagating its faith.

“We've seen the relative success of the hard-line civil society groups in pressing their agendas to the point where, in the aftermath of that Aceh training camp, a critique that emerged from within the jihadi organizations was, 'What have we achieved politically through jihadi operations?’ A big fat zero,” she said.

Since then she says there has been a growing connection between militant groups and Islamist organizations like the Islamic Defenders Front that do not overtly espouse violence.

Bonor Tigor Naipospos is with the Setara Institute, which monitors religious freedom in Indonesia. He says it is no coincidence that there has been a surge in violence against Christians and Ahmadiyah members.

Many Muslims consider the Ahmadiyah to be heretics, because although they consider themselves Muslims, they do not believe Mohammad was the last prophet.

Naipospos says radical groups have instigated the attacks to create a wider conflict.

“They hope they will get [a] reply from the Christian groups," he said. "They hope the Christian groups will reply with violence and then they will be justified in making the place of the conflict more bigger.”

While the government has been proactive in cracking down on terrorist groups, Jones says it has been slow to respond to the violence related to religious intolerance. The government has been passive, she says, because it perceives broad popular support in Indonesia, not for the violence, but for limiting other religious groups.

“I think there is a concern that there is a wider public perception that these people may be using tactics that we don't agree with, but their goals are more or less right," said Jones. "That is why we have the minister of religion making repeated statements about the need to ban Ahmadiyah and the fact that it is their own fault for getting attacked because they don't leave Islam.”

She says until the government takes strong action to prevent attacks or prosecute anyone who encourages violence, radical groups will continue to breed discontent and undermine the democratic foundations of the country.